Using RStudio on Hoffman2

Hoffman2 Happy Hour

Charles Peterson

🎉 Welcome to Hoffman2 Happy Hours

🎉 Welcome to the Hoffman2 Happy Hours

Short presentations on HPC-related topics and practical uses of Hoffman2

Thoughts for future “Happy Hour” topics? 💡

📧 cpeterson@oarc.ucla.edu

📖 Access the Workshop Files

This presentation and accompanying materials are available on UCLA OARC GitHub Repository 🔗 https://github.com/ucla-oarc-hpc

You can view the slides:

📄 PDF format - WS_H2HH-Rstudio.pdf
🌐 HTML Workshop Slides https://ucla-oarc-hpc.github.io/H2HH_rstudio
🎥 Recordings can be found on our BOX account

Clone the repository for workshop files:

git clone https://github.com/ucla-oarc-hpc/H2HH_rstudio

Clone the H2 Rstudio repository:

git clone https://github.com/ucla-oarc-hpc/H2-RStudio

RStudio Information

🖥️ What is Rstudio

A powerful IDE for R, data visualization, and script management

But why do you want to use RStudio on Hoffman2 when you can use your own computer???

RStudio on Hoffman2 provides access to:

Higher Memory
multi-core processing
GPUs
Your Hoffman2-hosted data

🌐 RStudio Formats

There are two main (free) RStudio formats that researchers can use

🖥️ RStudio Desktop

Standalone desktop application
Runs locally on the machine running R
Hoffman2 information on Desktop version

🌐 RStudio Server

Run RStudio as a server process
Runs R on a remote server
Connect to server and open on a web browser
Hoffman2 information on Server version

🚀 RStudio on Hoffman2

RStudio Desktop

Must connect to H2 via X11 forwarding or remote desktop
Runs R and Rstudio from H2 modules
sluggish interaction depending on connection

RStudio Server

R/Rstudio from Docker container
- Ran with Apptainer
- Workshop on using containers on Hoffman2
Isolate container OS image
- Separate version of R that was built from Hoffman2 modules
- **DON’T load R modules for server version

Running Rstudio Desktop

🖥️ Connect via X11

On your local machine, ensure you have an X11-enabled application installed:
- Windows: Use MobaXterm, XMing, or Cygwin. For WSL, install an X server like VcXsrv or XMing.
- macOS: Install and launch XQuartz.
- Linux: Ensure X11 forwarding is enabled on your terminal.

Use the following command to login to Hoffman2 with X11 Forwarding:

ssh -X USER@hoffman2.idre.ucla.edu

The -X flag enables your local computer’s X11 server to display the RStudio GUI.

🔗 Connect via Remote Desktop

Connect via Remote Desktop

Alternatively, you can use a remote desktop application:
NoMachine or X2Go: Configure the session with the correct server address and login credentials. Set the desktop resolution and environment based on your preferences.

Information on using X11 and Remote Desktop on Hoffman2 can be found on our workshop Visualization application on HPC

📜 Running Rstudio Desktop

Once connected to Hoffman2 via X11 or Remote Desktop,

Start an interactive session to request resources:

qrsh -l h_data=10G,h_rt=1:00:00

Load the necessary modules:

module gcc/10.2.0
module R/4.2.0
module load Rstudio

Launch RStudio:

module load Rstudio
rstudio &

If everything is set up correctly, the RStudio GUI will appear on your local computer or remote desktop.

Running Rstudio Server

🛠️ Starting RStudio

Get An Interactive Job

Containers cannot run on login nodes.

You MUST use a compute node

qrsh -l h_data=10G

Modify the qrsh to meet your RStudio computing needs

More memory and/or job time

qrsh -l h_data=50G,h_rt=5:00:00

More cores

qrsh -l h_data=10G -pe shared 10

Using GPUs

qrsh -l h_data=10G,gpu,V100

🛠️ Setting up directoreis

Create Temp Directories

Rstudio requires writable temporary directories outside of the container
It can be anywhere you have write access

Create directories in $SCRATCH/rstudiotmp

mkdir -pv $SCRATCH/rstudiotmp/{var/lib,var/run,tmp}

🛠️ Loading RStudio

Load the Apptainer Module

Apptainer is software that will run the Rstudio container

module load apptainer

RStudio Server on Hoffman2 created from Docker

Separate R from modules on Hoffman2
- DO NOT load R modules
- R packages may need to be reinstalled

🛠️ Starting RStudio

export RSTUDIO_VERSION=4.1.0
apptainer run \
      -B $SCRATCH/rstudiotmp/var/lib:/var/lib/rstudio-server \
      -B $SCRATCH/rstudiotmp/var/run:/var/run/rstudio-server \
      -B $SCRATCH/rstudiotmp/tmp:/tmp \
         $H2_CONTAINER_LOC/h2-rstudio_${RSTUDIO_VERSION}.sif

apptainer run
- Starts the RStudio container
-B $SCRATCH/rstudiotmp/[dir]:[/dir]
- Mounts tmp directories to the container
$H2_CONTAINER_LOC/h2-rstudio_4.1.0.sif
- Location of RStudio container
- Can be change to different RStudio versions

Information will display about RStudio session
- Note the compute node name and port number.
- Displays ssh -N -L ... info to be ran
- You will see a Rstudio Password
  - Needed to open Rstudio

Note

KEEP THIS TERMINAL OPEN UNTIL YOU JOB IS DONE

🛠️ Connecting to Rstudio

Once Rstudio process is started:

Open another terminal on your local computer
Run the port forward command
- Creates a connection from local computer to compute node

Change port 8787 if needed
nXXX is the compute node name
username is your Hoffman2 username

ssh  -N -L 8787:nXXX:8787 username@hoffman2.idre.ucla.edu

This will create a remote ssh connection from your local computer to the Hoffman2 compute node running Rstudio via port 8787

🛠️ Opening RStudio

Finally, open a web browser
- Type URL of RStudio Server
- Will ALWAYS be localhost
- Change port 8787 if needed

http://localhost:8787

⚡ Running Rstudio - The Easy Way

h2_rstudio.sh
- Script that runs everything from the previous slide
- Starts Rstudio and opens a web browser for you
- Runs on your local computer (not Hoffman2)

h2-studio.sh Information

Look at our Github page

Download script

wget https://raw.githubusercontent.com/ucla-oarc-hpc/H2-RStudio/main/h2_rstudio.sh
chmod +x h2_rstudio.sh

To display how to use this script

./h2_rstudio.sh -h

Run script
- Replace username with Hoffman2 username

./h2_rstudio.sh -u username

Tested Platforms

✅ Mac’s terminal app

✅ Window’s WSL2

✅ MoboXterm

❌ GitBash

📝 RStudio Script

This RStudio Script is currently on our GitHub page

This script will create an RStudio session on a compute node on Hoffman2.

REQUIRED OPTIONS:
  -u [username]    Your Hoffman2 username (mandatory)

OPTIONAL PARAMETERS:
  -m [MEMORY]     Memory requirements in GB (default: 10 GB)
  -t [TIME]       Time of RStudio job in HH:MM:SS (default: 2:00:00)
  -v [VERSION]    RStudio version (default: 4.1.0)
  -p              Request high-priority queue (highp)
  -g [GPUTYPE]    Request GPU resources, where GPUTYPE can be 'V100', 'A100', A6000, etc.

HELP:
  -h              Show this usage message

📦 Info on RStudio Container

Rstudio container was built using Docker
- Based on RStudio images from the Rocker Project
- Hoffman2 containers located at $H2_CONTAINER_LOC
- RStudio containers are named:
  - h2-rstudio_X.Y.Z.sif
  - Where X.Y.Z is the R version
View all available RStudio containers by running

module load apptainer
ls $H2_CONTAINER_LOC/h2-rstudio*sif

📍 User Packages

Separate build of R and
R packages installed in unique directory
- ~/R/APPTAINER/h2-rstudio_4.1.0 (for h2_rstudio-4.1.0.sif)
HPC Container files
- Docker and definition files for Hoffman2 containers
- RStudio Dockerfiles have all you need to build RStudio

R Package Installs

Some R packages require extra libraries or software in the container
Contact us to update this container
- OR you can modify the Dockerfile for your own container

🛠️ Error fixing

If Rstudio does not at start up
- Possibly due to previous RStudio not shutdown correctly
Clear out any tmp directories files

rm -rf $SCRATCH/rstudiotmp 
mkdir -pv $SCRATCH/rstudiotmp/{var/lib,var/run,tmp}

Clear out RStudio config files

rm -rf $HOME/.config/rstudio
rm -rf $HOME/.local/share/rstudio

🖥️ Terminal Access

Access to a Hoffman2 terminal in RStudio

📊 Using Batch R

Instead of interactive RStudio, you can run R as a non-interactive batch job
- Use R from inside RStudio container as a qsub job
Create job script

#!/bin/bash
#$ -cwd
#$ -o rstudio_batch.out.$JOB_ID
#$ -j y
#$ -l h_rt=3:00:00,h_data=10G
#$ -pe shared 1

# Load the apptainer module
. /u/local/Modules/default/init/modules.sh
module load apptainer

# R Version
export RSTUDIO_VER=4.4.0

# Use the RStudio container to run R code
apptainer run $H2_CONTAINER_LOC/h2-rstudio_${RSTUDIO_VER}.sif R CMD BATCH myRtest.R

Then run this job script

qsub rstudio_batch.job

📝 Summary

RStudio Desktop on Hoffman2
- Connect via X11/Remote Desktop
- Runs R from H2 modules
RStudio Server on Hoffman2
- Access through on your web browser
- Runs R from inside containers

🙏 Thanks and Happy Computing!

Questions? Comments?

📧 cpeterson@oarc.ucla.edu
Look at for more Hoffman2 workshops and other OARC workshops